jazzy

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.. image:: https://raw.githubusercontent.com/AstraZeneca/jazzy/master/docs/_static/jazzy.png :width: 400 :alt: Jazzy

|PyPI| |Status| |Python Version| |License|

|Read the Docs| |Tests| |Codecov|

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.. |PyPI| image:: https://img.shields.io/pypi/v/jazzy.svg :target: https://pypi.org/project/jazzy/ :alt: PyPI .. |Status| image:: https://img.shields.io/pypi/status/jazzy.svg :target: https://pypi.org/project/jazzy/ :alt: Status .. |Python Version| image:: https://img.shields.io/pypi/pyversions/jazzy :target: https://pypi.org/project/jazzy :alt: Python Version .. |License| image:: https://img.shields.io/pypi/l/jazzy :target: https://opensource.org/licenses/Apache-2.0 :alt: License .. |Read the Docs| image:: https://img.shields.io/readthedocs/jazzy/latest.svg?label=Read%20the%20Docs :target: https://jazzy.readthedocs.io/ :alt: Read the documentation at https://jazzy.readthedocs.io/ .. |Tests| image:: https://github.com/AstraZeneca/jazzy/workflows/Tests/badge.svg :target: https://github.com/AstraZeneca/jazzy/actions?workflow=Tests :alt: Tests .. |Codecov| image:: https://codecov.io/gh/AstraZeneca/jazzy/branch/master/graph/badge.svg?token=4HCWYH61S5 :target: https://codecov.io/gh/AstraZeneca/jazzy :alt: Codecov .. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white :target: https://github.com/pre-commit/pre-commit :alt: pre-commit .. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg :target: https://github.com/psf/black :alt: Black

Full Author List

• Eike Caldeweyher
• Gian Marco Ghiandoni

Introduction

Jazzy is an efficient computational tool for the calculation of hydration free energies and hydrogen-bond acceptor and donor strengths. A publication describing the implementation, fitting, and validation of Jazzy can be found at doi.org/10.1038/s41598-023-30089-x_.

| If you are using Jazzy in your research, please remember to cite our publication as: | Ghiandoni, G.M., Caldeweyher, E. Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules. Sci Rep 13, 4143 (2023)

Features

• Hydration free energies
• Hydrogen-bond strengths
• Visualisation functions (SVG)
• Application programming interface
• Command-line interface

Installation via PyPI

You can install Jazzy via pip_ from PyPI_:

.. code:: console

$ pip install jazzy

Installation via Poetry (for development)

Requirements to install Jazzy from the code repository:

• poetry_
• pyenv_ or conda_
• python>=3.6

First check that poetry is running (v1.4.1 at March 2023)

.. code:: console

$ poetry --version Poetry version v1.4.1

Create a virtual environment (via pyenv or conda) and activate it. Afterwards, clone the Jazzy project from GitHub and install it using poetry.

.. code:: console

$ git clone [email protected]:AstraZeneca/jazzy.git $ cd jazzy $ poetry install

If you wish to replicate our parameter fitting (see data/optuna_fitting and optimisation), you need to install the specific version of optuna. At the time of the study, we used optuna==2.3.0. You can install that manually using pip or poetry.

.. code:: console

$ poetry install --with optuna $ pip freeze | grep optuna optuna==2.3.0

Usage and Cookbook

Please see the Usage <Usage_>_ and Cookbook <Cookbook_>_ sections for details.

Contributing

Jazzy is an open project in every shape and form, thus feedback on how to improve its documentation or functionalities is always welcome. To learn more, see the Contributor Guide_.

License

Distributed under the terms of the Apache 2.0 license_, Jazzy is free and open source software.

Issues

If you encounter any problems, please file an issue_ along with a detailed description.

Credits

This project was generated from @cjolowicz's Hypermodern Python Cookiecutter template.

.. _@cjolowicz: https://github.com/cjolowicz .. _Cookiecutter: https://github.com/audreyr/cookiecutter .. _Apache 2.0 license: https://opensource.org/licenses/Apache-2.0 .. _poetry: https://python-poetry.org/docs/#installation .. _pyenv: https://github.com/pyenv/pyenv#installation .. _conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html .. _PyPI: https://pypi.org/ .. _Hypermodern Python Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python .. _file an issue: https://github.com/AstraZeneca/jazzy/issues .. _pip: https://pip.pypa.io/ .. _doi.org/10.1038/s41598-023-30089-x: https://doi.org/10.1038/s41598-023-30089-x .. github-only .. _Contributor Guide: contributing.rst .. _Cookbook: https://jazzy.readthedocs.io/en/latest/cookbook.html .. _Usage: https://jazzy.readthedocs.io/en/latest/usage.html